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Description/Abstract

Various physical mutation-scanning methods have been developed to avoid unnecessary resequencing of long stretches of DNA (1)(2)(3)(4)(5)(6). Protein-based mutation-scanning techniques include enzymatic digestion [reviewed in Ref. (7)], protein binding to a DNA duplex, and direct analyses of the in vivo or in vitro gene product. One such enzyme is T4 endonuclease VII (endoVII), the product of gene 49 of bacteriophage T4 (8). Radiolabel replacement with fluorescent tags has facilitated automated analysis (9). EndoVII recognizes heteroduplex structural distortions, nicking 2–6 bp 3' to the distortion, with efficiency dependent on sequence context (10) and mismatch type(11). Perfectly matched DNA undergoes some background digestion, which produces a highly reproducible pattern (12). Mutation detection sensitivity obtained with endoVII digestion was found to be similar to that for denaturing HPLC and direct sequencing (13).

Microplate array diagonal gel electrophoresis (MADGE) (14) provides an open-faced 96-well gel format for polyacrylamide gels. Recently, nondenaturing 192-, 384-, and 768-well formats of MADGE for high-throughput checking of PCR and post-PCR reactions (15) have been developed. We have combined, in proof-of-principle experiments, the mismatch digestion properties of endoVII with the high-throughput capabilities of MADGE and a newly developed denaturing MADGE format to create a simple mutation-scanning technique that can screen 1000 PCR samples during a single 35-min electrophoretic run.